I am trying to get Calibre to work with the books in my Nook standard, but all I get is "This book is protected by DRM".

You can add books to calibre's library that are restricted by DRM. You can use calibre to send them to your device, but calibre can't view or convert these books. If you are interested in removing the restriction you can find information by searching Apprentice Alf's Blog (look for tools_2.4.zip, instructions inside archive).

Mobileread is not a forum where detailed descriptions on removing DRM are discussed.